Utilizing the X Chromosome for Deep Ancestry by Kathy Johnston (For 23andMe Complete Edition testers, Family Tree DNA X-Chromosome testers, and any other company that provides X-STR results,  i.e. deCODEMe, etc.  23andMe and deCODEme do SNP testing not X STR testing, FTDNA does X-STR testing ) X-Chromosome Deep Ancestry If you are interested in deep (really deep) ancestry, then you will want to contribute your X chromosome information to our X chromosome study group. There are some genes that are related to health information on your X-chromosome but we leave those genes off of the World Families website. There are haplogroups on the X that scientists really have not yet named similar to the H, U, K of mitochondrial DNA and the R, J, I etc. of Y-chromosome DNA. For those who love finding and discussing SNPs, there are plenty of specific unique event polymorphisms. These are likely related to variable STR results nearby that have not yet been reported and compared in many people at a DNA testing company. The X can probably be studied similar to the Y with subclade divisions easy to determine. There are just more crossover recombinations to deal with and the inheritance patterns are different. It is difficult to combine the similarities in a spread sheet because each of us has multiple subclades spliced together. We have found some STRs associated with specific haplogroups determined by SNPs but we are not a lab testing company so we are really at the mercy of the data at hand. The X is useful in family and paternity studies but that is not what we are doing with it so far. People can report their X STRs tested at Family Tree DNA though to our World Families group. We have interspersed a few of these STRs of interest among the SNPs in the SNP spread sheet to show correlations but we need more people who have both SNP and STR results in order to show the relationships. In some cases, it is possible to study continent specific and geographical origins by looking at haploblock patterns. Anders Paulsen and David Faux are attempting to identify regional SNP haplotypes of Native Americans. David has reason to believe that he inherited significant X chromosome blocks from a Native American ancestor. A year ago we were hoping to find a lot of geographical associations, but we mostly saw very ancient blocks dispersed over wide areas. I found that about 20% of Europeans do not match the Asians at all in one of our blocks (in Xq12) but come much closer to matching the Africans. So one question we hope to answer is: what does that mean in terms of ancient migrations? That same information is also available by studying the HapMap groups of populations online. Then there are the crossover points that show up in several different people. So, another question we are asking is how can we determine the time to most recent crossover? These are unique-event-crossovers unless you just want to call these hot spots. These are specific points that are repeated in many populations and I don't know of any published articles on this topic. Submitting your X results Visit: http://www.worldfamilies.net/forum/index.php?topic=8438.0 which tells you how to submit your X chromosome results to Ben Moscia and/or to Sean MacGorman Powell. Don't forget to let them know the geographical origins of your X, if known. Remember not to include any geographic populations that have two males in a row in your pedigree. For a visual aid, see http://www.thegeneticgenealogist.com/wp-content/uploads/NewChart5.jpg If your genealogy program can print an ahnentafel chart, Ann Turner has prepared a file with the relevant ahnentafel numbers. http://dnacousins.com/AHN_X.TXT Current Studies by Volunteers to Identify New X Haplogroups I am particularly interested in our two main haplotype groups at http://www.worldfamilies.net/geo/xdna/results?raw=1 between these two markers: 66,228,526 (= rs1567524) 66,564,941 (= rs2497928) For beginners, I will simplify the groups so please check your raw data: Anyone with a rare T at 66,269,421 rs1397631 is likely to have an X chromosome in the red with sub-set blue group. For 66,238,687 ( = rs4827392) A is yellow, C is red For 66,480,739 ( = rs2497939) A is yellow, C is red If you switch from A to C or C to A, you are in a crossover group, usually yellow to red.   The majority of people will be yellow, a minority red. Women who are AC then AC are very likely to have one yellow and one red, but not always. Check to see if you have many non-matching pairs throughout this sequence and also check for the blue T above. Those of us in the red-blue group or in a crossover group are even more rare and I happen to have one X of each so that is why I am so interested in these uncommon haplotypes. Females will be scrambled if your parents' X chromosomes do not match. However, within this particular area of the chromosome, the crossovers are extremely rare so you can usually phase (unscramble) your two haplotypes. I will help any female determine her probable two haplotypes in our Xq12 area starting with position 66,228,526 since this is easy to do just by a quick glance if you are from an Asian, Near East or European population. Send me an e-mail if you need help. If both of a female's Xs are from an ancient African tribe, then there may be too much diversity for me to extract the data, but for most genealogists ordering these tests, our ancestors were relatively recently bottlenecked. There are two clear main haplotypes, so perhaps a major disaster like a great flood really happened causing the bottleneck. The actual two sequences are much older than that and seem to represent two different subspecies or species of our very ancient ancestors, however. Recent phasing of some of our African American female genealogists have revealed that if a common European X sequence is subtracted from the X pairs, a very nice African appearing sequence appears. This can be useful in identifying origins of recent ancestral lines and may end up showing some African markers that are distinct from European markers. For people with such divergent admixtures, the X chromosome may be useful to identify the background of recent ancestors. If you are a female who has just one chromosome that has crossed over in a rare recombination event sometime in the past, then usually you will see matching between your two Xs at a specific location within this block. Phasing You can see how the female's X data is reported for two chromosomes. Then you should compare that to a male's X sequences in the raw data. It will help you to understand phasing of the autosomes and half identical matches later on. See Ann Turner's phasing article here: http://www.jogg.info/42/files/turner.pdf X Chromosome Inheritance Tutorial Here is a demonstration of X Chromosome inheritance: http://www.smgf.org/education/animations/x_chromosome.jspx Page compiled on: 01 Dec 2009 Contribution credits: Kathy Johnston Copyright © 2005-2009 ISOGG.org All Rights Reserved